- Episode 1: Mockery in the Moon
- Music from Super Mario World 2: Yoshi's Island plays during the prologue scene.
- Music from Banjo-Kazooie plays during Twilight's visit to Sweet Apple Acres.
- When Rainbow clears the clouds in under ten seconds flat, an instrumental of the Sonic the Hedgehog (SatAM) theme plays to emphasize her statement of being "The fastest thing alive!"
- Fluttershy leads her chorus of birds in singing the theme song to The Andy Griffith Show
- Episode 2: Elements of Parody
- The RPG battle finishes with Fluttershy using Esuna to heal the manticore.
- Said battle also takes elements and sound effects from both Super Mario RPG and EarthBound.
- Steven Magnet laments that he'll never be able to "top that scientist fellow at this year's Mustache-Off". Given the creators' previous work, he's probably talking about Dr. Eggman.
- The Shadow Bolts offer Rainbow Dash her own spin-off series, but she loses interest when they mention she'd "[play] in a band, and use music to save the world from evil."
- Music from Tengen Toppa Gurren Lagann plays when Twilight figures out how to activate the Elements of Parody, their activation is accompanied by the power-up sound effects from Dragon Ball Z, and the main characters proceed to blast Nightmare Moon with a "Giga Parody Breaker".
- Amusingly enough, Princess Celestia's return is accompanied by the same music as that of another missing princess.
- Episode 3: Call of the Creepy
- Diamond Tiara and Silver Spoon are always accompanied by Scanty and Kneesocks's leitmotif. Their introduction even cues a drawing of them in the show's style.
- Doctor Whooves tries to get out of buying apples by saying he's got "four things and a dragon" to deal with.
- Rainbow Dash tries to brush off Apple Bloom by saying "I've got places to go, gotta follow my rainbow and all that", a nod to the lyrics of "City Escape" from Sonic Adventure 2.
- The "Eighties training montage" includes a parody of the intermission scene from Punch-Out!!, complete with appropriate music.
- "We're making cupcakes! The delicious treat, silly, and not the horrible abomination that corrupts your perception of everything you know and love!"
- Applebloom attempts to escape the party Metal Gear Solid style, complete with matching Game Over screen.
- Sweetie Belle's Foul Flank censor is a ponyfied version of the Laughing Man's logo. Scootaloo's is the "Can't Show!" sign.
Shout Out / My Little Pony: Camaraderie Is Supernatural